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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtacttaaaaggtgatttagcctctccccgatatcttcctggcccctgggagcaattcagccccctattccagaatattgacaaagctgttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAGGATGGTCTCCGGGAACTTGAGGAGGCTGAGATTGATGAATATGTTGCTG

Basic information

species Zea mays
transcript GRMZM2G138128_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138128_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
tgtacttaaaaggtgatttagcctctccccgatatcttcctggccc--ctgggagcaattcagcccc-ctattccaga-atattgacaaagctgttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAGGATGGTCTCCGGGAACTTGAGGAGGCTGAGATTGATGAATATGTTGCTG
|||  ||      ||      |        | ||| |   ||       |  ||    ||  | |   | ||| | ||   | ||||| |    || |  | |||||||||| ||||| || |||||||||||| |||||||||||||| ||||||||||||| ||  |||| ||||||||||| || || |||||||||||||
tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaactgacataa--attgc--acagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG

upper sequence: GRMZM2G138128_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G23580.1 (Glycine max), 3'ss of exon 2
-----tgtacttaaaaggtgatttagcctctccccgatatcttcctg-gcccctgggagcaattcagccccctattccagaatattgacaaagctgttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAGGATGGTCTCCGGGAACTTGAGGAGGCTGAGATTGATGAATATGTTGCTG
     |||     ||      | |  |   |  |  ||| |||  |  ||  ||       | |  |     ||| |   | | |||||     | ||| |  ||||||||||| ||||| ||||||||||| || ||||| |||||||| ||| || | ||||| ||  |||| ||||| || || |||||||     |||||||
attcctgttgcataattacagtatttctgtttgctaatagcttgttatgcgtctcaacaggaatatgtttaatatacttcacttttgac----tttttaat--tagGTTGTTGAGAGTGGAGGGAAGAACATAGAAGTTGCGGTGATGACTAAGGAGCAGGGTCTGCGTCAACTGGAGGAAGCCGAAATTGATGCCATCGTTGCTG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211387067|gb|FL031636.1|FL031636
EST:     AGACCTCCGGCAAGGAGGCCATCAAGCTTGCTATTCGTGCACTTCTAGAG                         GTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG
genomic: AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAGgtatatcata ... ttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG
EST: gi|149051858|gb|EE155986.2|EE155986
EST:     AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAG                         GTTGTTGGAAAGTGGTGGGAAGAACATCGAGGGTGCAGTGATGACAAAGAA
genomic: AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAGgtatatcata ... ttactgatagGTTGTTG-AAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAA
EST: gi|211304635|gb|FL018755.1|FL018755
EST:     AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAG                         GTTGTTGAAAGTGGTGGGAAGA-CATCGAGGTTGCAGTG
genomic: AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAGgtatatcata ... ttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTG
EST: gi|148952506|gb|EC898333.2|EC898333
EST:     AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAG                         GTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG
genomic: AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAGgtatatcata ... ttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG
EST: gi|67039736|gb|CO465991.1|CO465991
EST:     AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAG                         GTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG
genomic: AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAGgtatatcata ... ttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG
EST: gi|91873762|gb|EB403719.1|EB403719
EST:     AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAG                         GTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG
genomic: AGACCTCCGGCAAGGAGACCATCAAGCTTGCTATTCGTGCACTTCTAGAGgtatatcata ... ttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgggagcaattcagccccctattccagaatattgacaaagctgttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAGGATGGTCTCCGGGAACTTGAGGAGGCTGAGATTGATGAATATGTTGCTG
                               tattgac  putative branch site (score: 2)
                           agaatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtacttaaaaggtgatttagcctctccccgatatcttcctggcccctgggagcaattcagccccctattccagaatattgacaaagctgttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAGGATGGTCTCCGGGAACTTGAGGAGGCTGAGATTGATGAATATGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG